The churning brown water that surges off roads and parking lots in the District of Columbia during rainstorms is a visible sign of trouble for the Potomac and Anacostia rivers. Underground and out of sight, there's another problem.

A labyrinth of pipes beneath the city catches the stormwater and moves it toward the Potomac River. Below one-third of the District, stormwater in these pipes combines with raw sewage.

During periods of heavy rain, the system overflows with a distressing mix of untreated stormwater and sewage. The excess pours through outfall points directly into the Anacostia River, Potomac River and Rock Creek. It also overwhelms the advanced wastewater treatment plant at Blue Plains. ...

Not so long ago, Maryland had so many oyster shells that Eastern Shore residents used them to pave driveways.

But that began to change in the 1980s, when oyster harvests began their slide to today's historic lows. Instead of harvests in the millions, watermen are lucky to catch around 100,000 bushels a season.

Today, one of the biggest problems in reviving oyster populations is an acute lack of shells with which to build new habitat. But a new effort is recycling shells off dinner plates at restaurants or catered affairs. ...

My friend Tom Wisner chose a fine April afternoon to slip from his hospice bed in southern Maryland. Redbud and shadbush were abloom and the last of winter's tundra swans were pulling out for Alaskan nesting grounds. Rockfish swelling with roe and milt were thrusting up tributary rivers; blue crabs down in Virginia were rising from the mud. Ospreys were nest building and young eagles learning to fish. A good time to be alive, Tom might have said, looking back, chuckling.

Forty years of performing for a living, celebrating the Bay region in story and song, and four CDs, including the anthem "Chesapeake Born," had earned him the title "Bard of the Chesapeake." Some just called him "The Wiz." ...

Representatives from several states expressed misgivings about the time frame for developing a new Bay cleanup plan at a recent meeting of high-level officials, but EPA representatives insisted the agency will stick to its schedule to complete a new strategy by the end of the year.

Technical issues have mounted in the development of the plan, known as a Total Maximum Daily Load, particularly with the updated computer models used to estimate the amount of pollution reductions needed from each state and river to clean the Bay. ...

A new study estimates that current manure application guidelines in approved nutrient management plans provided to farmers result in tens of millions of pounds of excess phosphorus being applied to croplands in the watershed, greatly increasing the risk of pollution to local waterways and the Bay.

The study estimated that manure containing about 37 million pounds of phosphorus beyond what's needed to grow crops was applied to fields in the 11 counties with the most intense animal agriculture within the Bay watershed annually. ...

The EPA in April ordered 79 municipalities in southcentral Pennsylvania to improve their stormwater management programs to help protect local waterways and the Bay.

A lengthy review by the agency found that a third of the stormwater management programs in the state's southcentral region had "more than minimal deficiencies" with annual reports they are required to file, said Andy Dinsmore, stormwater team leader within region's pollution-discharge enforcement branch.

In their annual report, municipalities are required to provide information on six minimal control measures covered in their stormwater permits, but many described no actions or, in some cases, appeared to cut and paste the same response year after year. ...

The Bay's underwater grass beds surged 12 percent last year to the second highest level observed in recent decades.

Overall, the annual survey mapped 85,899 acres, up from the 76,860 acres mapped in 2008. Still, acreage was less than halfway to the Baywide goal of 185,000 acres. The goal is based on the amount of grasses observed around the Bay in the past.

Scientists cautioned that much of the increase was driven by a large proliferation of widgeon grass in the mid-Bay.

Widgeon grass is notorious for expanding rapidly when conditions are good, then disappearing just as rapidly when water quality worsens, contributing to the often wide fluctuations in Bay grass acreage. ...

The Chesapeake Bay blue crab population has soared to levels not seen in more than a decade, raising optimism that dramatic harvest reductions implemented two years ago are beginning to show results.

The annual winter dredge survey estimated the number of crabs in the Bay at 658 million, a 60 percent increase from last year, and the highest level seen since 1997. Data from the survey showed that the number of spawning age females, adult males and juvenile crabs all rose.

Scientists and officials credited the surge to the controversial restrictions enacted in 2008 aimed at slashing the harvest of female crabs by one-third. ...

Bay cleanup efforts may have, literally, been fighting a headwind almost from the day they started.

For years, scientists have been confounded by a Bay restoration paradox. Although the amount of nitrogen entering the Chesapeake has declined somewhat, the extent of low-oxygen waters-so-called "dead zones"-has increased.

New research offers a surprising explanation. Malcolm Scully, an assistant professor at Old Dominion University, suggests that a multi-decadal climate cycle has altered the region's wind patterns during spring and early summer months in a way that exacerbates the Bay's dissolved oxygen problems. ...

On a brisk spring day, Arthur Allen parks his car, straightens his cap and gets to work. He walks across rows of corn stubble and weeds, his black dress boots no worse for the wear. Finally, he reaches his destination: a line of plastic tubes used to measure how much nitrogen and phosphorus is seeping into the fields.

For two decades, Allen and a team of researchers have been toiling quietly on this one-time poultry farm in Princess Anne to discern which farming methods do the best job of reducing the amount of nutrients that builds up in the soil and eventually drains into the Manokin River watershed, which reaches the Chesapeake Bay. ...